So I would tell the theme author to fix those things first as they might cause you potential problems later down the line. Not too mention, it's a royal mess of calling everything jQuery under the sun. Themeforest themes are really not coded well, sorry to say that to you.

But I think the main problem is WP E-commerce and their use of a custom Thickbox.js here:

I have no idea why they ship their own version when it's available in WordPress and we call it locally from the core folders of WordPress for our popup. Plus, there's another version of a fancy box loading with your theme here: